FreeBSD update software and apply security patch

You can list outdated ports list with pkg_version command:pkg_version -vIL=

Update FreeBSD packages / software

Now run portmanager to upgrade installed ports:portmanager -u -l

How do I upgrade a single software only?

portmanager allows you to update a single port and all of its dependencies. For example update port called bash i.e. bash shell (shells/bash), enter:portmanager shells/bash -l -u

How do I apply binary security updates for FreeBSD?

Latest version includes a tool called freebsd-update (thanks to Bok for pointing out this tool). The freebsd-update tool is used to fetch, install, and rollback binary updates to the FreeBSD base system.
Fetch updates

Use fetch option to get all available binary updates:freebsd-update fetch